Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010921.1 Corchorus capsularis cultivar CVL-1 contig10942, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8365
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3743 original size:33 final size:33
Alignment explanation
Indices: 3702--3814 Score: 140
Period size: 33 Copynumber: 3.4 Consensus size: 33
3692 GCCGCGCAAC
3702 ACCGGCCACACGACATGGACATGTCCGGCCATC-
1 ACCGGCCACACGACATGGACATGTCCGGCCA-CA
* *
3735 ACCGGCCACGCGACATGGACATGTCCGGCTACA
1 ACCGGCCACACGACATGGACATGTCCGGCCACA
* * *
3768 ACCGGCCAAACGAC-TCGGCCATGCCCGGCCACA
1 ACCGGCCACACGACAT-GGACATGTCCGGCCACA
*
3801 ACCGGCCACGCGAC
1 ACCGGCCACACGAC
3815 CCTTTGTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.03
33 67 0.97
ACGTcount: A:0.24, C:0.42, G:0.26, T:0.09
Consensus pattern (33 bp):
ACCGGCCACACGACATGGACATGTCCGGCCACA
Found at i:6006 original size:5 final size:5
Alignment explanation
Indices: 5996--6028 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
5986 AATTAACTAA
5996 TAAAC TAAAC TAAAC TAAAC T-AAC TAAAC TAAA
1 TAAAC TAAAC TAAAC TAAAC TAAAC TAAAC TAAA
6029 TTAATAGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAC
Found at i:6022 original size:9 final size:9
Alignment explanation
Indices: 5998--6027 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5988 TTAACTAATA
5998 AACTAAACT
1 AACTAAACT
6007 AAACTAAACT
1 -AACTAAACT
6017 AACTAAACT
1 AACTAAACT
6026 AA
1 AA
6028 ATTAATAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (9 bp):
AACTAAACT
Found at i:6231 original size:30 final size:30
Alignment explanation
Indices: 6195--6256 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
6185 TTGGGTAGTG
6195 AACACCCGTCGGCACTTCACTCACCCAATC
1 AACACCCGTCGGCACTTCACTCACCCAATC
6225 AACACCCGTCGGCACTTCACTCACCCAATC
1 AACACCCGTCGGCACTTCACTCACCCAATC
6255 AA
1 AA
6257 ATTCATTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.45, G:0.10, T:0.16
Consensus pattern (30 bp):
AACACCCGTCGGCACTTCACTCACCCAATC
Found at i:6285 original size:18 final size:19
Alignment explanation
Indices: 6248--6285 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6238 ACTTCACTCA
* *
6248 CCCAATCAAATTCATTAAG
1 CCCAATCAAATTAATCAAG
6267 CCCAATC-AATTAATCAAG
1 CCCAATCAAATTAATCAAG
6285 C
1 C
6286 TATCACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (19 bp):
CCCAATCAAATTAATCAAG
Found at i:7930 original size:103 final size:103
Alignment explanation
Indices: 7746--7940 Score: 293
Period size: 103 Copynumber: 1.9 Consensus size: 103
7736 TGCATACTCG
*
7746 TAATTTTGGGTCATGACTGACACGAAGGTTGATATTTGTGATACCGAACCCCGTGTACTCCACTT
1 TAATTTTGGGTCATGACTGACACGAAGGTTGATATTTGTGATACCGAACCCAGTGTACTCCACTT
7811 CCCAAAAACAGCGGAGTAATTTATTAAGATGCTTTGCA
66 CCCAAAAACAGCGGAGTAATTTATTAAGATGCTTTGCA
* * * ** *
7849 TAATTTTGGTTCGTGACTGACGC-ATAGGTTGATATTTGTGATATTGAACCCAGTGTGCTCCACT
1 TAATTTTGGGTCATGACTGACACGA-AGGTTGATATTTGTGATACCGAACCCAGTGTACTCCACT
* *
7913 TCCCAAAAACAGTGGAGTAGTTTATTAA
65 TCCCAAAAACAGCGGAGTAATTTATTAA
7941 ATTTCCTCTT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 1 0.01
103 81 0.99
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (103 bp):
TAATTTTGGGTCATGACTGACACGAAGGTTGATATTTGTGATACCGAACCCAGTGTACTCCACTT
CCCAAAAACAGCGGAGTAATTTATTAAGATGCTTTGCA
Done.